Peptide

Peptide sequence objects and functions.

Peptide dataclass

Peptide sequence object.

Parameters:

Name	Type	Description	Default
sequence	str	peptide amino acid sequence	required
mapped_proteins	list[str]	list of proteins the peptide sequence maps to	[]

Attributes:

Name	Type	Description
sequence	str	Peptide sequence from peptide network
mapped_proteins	list[str]	list of all proteins mapping to sequence

Source code in src/xlranker/bio/peptide.py

@dataclass
class Peptide:
    """Peptide sequence object.

    Args:
        sequence (str): peptide amino acid sequence
        mapped_proteins (list[str]): list of proteins the peptide sequence maps to

    Attributes:
        sequence (str): Peptide sequence from peptide network
        mapped_proteins (list[str]): list of all proteins mapping to sequence

    """

    sequence: str
    mapped_proteins: list[str]

    def __init__(self, sequence: str, mapped_proteins: list[str] = []):
        """Initialize the Peptide object with a sequence and mapped proteins.

        Args:
            sequence (str): amino acid sequence
            mapped_proteins (list[str], optional): list of protein names this sequence maps to. Defaults to [].

        """
        self.sequence = sequence
        self.mapped_proteins = mapped_proteins

    def __str__(self) -> str:
        """Get the string representation of this peptide.

        Returns:
            str: the amino acid sequence of this peptide.

        """
        return self.sequence

__init__(sequence, mapped_proteins=[])

Initialize the Peptide object with a sequence and mapped proteins.

Parameters:

Name	Type	Description	Default
sequence	str	amino acid sequence	required
mapped_proteins	list[str]	list of protein names this sequence maps to. Defaults to [].	[]

Source code in src/xlranker/bio/peptide.py

def __init__(self, sequence: str, mapped_proteins: list[str] = []):
    """Initialize the Peptide object with a sequence and mapped proteins.

    Args:
        sequence (str): amino acid sequence
        mapped_proteins (list[str], optional): list of protein names this sequence maps to. Defaults to [].

    """
    self.sequence = sequence
    self.mapped_proteins = mapped_proteins

__str__()

Get the string representation of this peptide.

Returns:

Name	Type	Description
str	str	the amino acid sequence of this peptide.

Source code in src/xlranker/bio/peptide.py

def __str__(self) -> str:
    """Get the string representation of this peptide.

    Returns:
        str: the amino acid sequence of this peptide.

    """
    return self.sequence